Anyway, according to my consultant my “CT is fine and kidneys fine too”, which is very good news indeed. At this point it’s 3 years since my diagnosis (34 months since my cancer operation) and the odds against me having a reoccurrence are improving all the time.

And although my left kidney was showing as dilated, it seems that that isn’t stopping the kidney from working normally (or close enough to normally that the doctors are happy to leave well alone). Which is more great news.

So now we just have to concentrate on finding a way to get the wound tracks in my pelvis to continue healing so I can (eventually) get my ileostomy reversed again, and hopefully put the last of this behind me.

It’s not really that anything has radically changed, but time is passing. The constant fighting with the ileostomy, the lack of sleep and consequent tiredness, the limits on what I can physically do while I’ve got the ileostomy. Trying to cope with the frustrations of the treatment not working as planned. Not being able to move on with my life plan in some of the ways that I would like to. It all adds up. And wears me down.

I noticed that on the 26th it will have been 3 years that I’ve been fighting this, and I’ve realised that actually I’m never really going to be able to completely stop, because even if we do finally solve my current problems, I’ll still never completely recover back to the level of wellness that most people take for granted.

Meanwhile, because I’m basically coping with being back at work and I’m getting pretty good at hiding the outward signs of my condition, there seems to be an expectation that I can do all the mad things that everyone else is expected to do again. Which actually, I can’t. Fortunately my immediate colleagues shield me from some of the worst excesses of the IBM system – but it’s frustrating that they have to.

For the first time I have found myself wondering if I should declare myself “disabled” to the IBM HR machine. I guess it all hinges on your definition of disabled. I’ve never considered myself to be disabled – there are people in much worse situations than me – but I’m starting to wonder if I need that label to maintain awareness. It feels like a very large step though, and one I’d really rather not take. Somehow it also feels like giving in.

And in other news, my appointment for the MAG3 Renogram is now through for Thursday morning. The fight goes on.

Sadly the conversation wasn’t great. After the last intervention in May, I made good progress, with clear signs of healing of the wound tracks all the way through to August. But from August to November there was no further sign of healing in the wound tracks. On the positive side, at least the general inflammation in my pelvis continued to reduce steadily.

So the conversation centered around what we could do to try to get continued healing in the wound tracks, and possible issues and side effects associated with each of those options.

As always, the backstop to all this is to have a permanent colostomy. However, my consultant was very clear that this is not a simple option either. His comment was that it would be a bigger and more difficult operation to recover from than my original cancer operation. His estimate was several months off work to recover from it. So neither he nor I are keen on that option (for slightly different reasons!) until there is nothing else left.

So it’s really a matter of trying to find a way to restart the healing in the wound tracks. Long term antibiotics may help, but have their own problems. In particular, the kinds of antibiotics that would help will give me nerve damage if used long term – which of course, is exactly what we are thinking about. So the question is, where exactly is the trade-off? Of course I’d sacrifice temporary nerve damage for a successful result. What about permanent nerve damage? How much? What if I get the permanent nerve damage but no successful result? It’s a minefield.

Other options revolve around further surgery to open up the wound tracks more, trying to improve the long-term healing. That might work, especially in conjunction with more regular currettage and some antibiotics. Or it might not. My consultant just doesn’t know.

But unless we can find a way to move forward then my options are starting to look very limited indeed. Which is not good news.

But in the short term it’s time for my 3rd annual cancer check-up, so I’m due another full-body CT scan with the nasty IV contrast agent. And in the meantime my consultant will go off and consult with his colleagues and try to work out the best way forward for me.

Fun for all.

In common with the IVU test, the urologist can determine problems with blood flow through each kidney, as well as problems with the drainage from each kidney to the bladder, showing the location of any blockage or restriction. However, in addition it is possible to measure the relative and absolute efficiency of each kidney, which can be useful in determining whether or not kidney function is impacted to the point where intervention is required or not.

If I get to the point where it is required, the question will be what level of intervention I can cope with. Options involving stents are only temporary, and require a general anaesthetic each 6 months to renew them. Not good. Options with balloons to “stretch” the tissues around a restriction to open up the ureter tend to be limited in effectiveness. I’m told that the gold standard is normally to “replumb” the ureter, but that’s going to be a massively difficult undertaking in my pelvis thanks to all my previous surgery. Not ideal.

But if the kidney function is sufficiently degraded for long enough then the kidney will eventually shut down. At that point it’s normal to remove the kidney. Apparently you can get by on less than half a kidney, so losing one isn’t the end of the world. But again, removing one of my kidneys is going to be a lot harder than normal.

So right now I’m hoping for a test result that shows my kidney function is good enough to not require any action at all.

It replaced my original 760CD, and like that machine, I carried it with me on numerous business trips all over the world. It survived being dropped, splashed with coffee, slung into bags, and then crammed into overhead luggage racks or under seats where it invariably got stood on. Despite all this abuse it still worked faultlessly in temperatures as varied as -20c in the Scandinavian winter, through to +40c in the humid summers of the US Deep South.

When IBM supplied me with an upgrade I bought my 600 off the company. For a time it was my personal system. Then it ran my home network, 24×7 until I could afford the parts to build a proper server. It was my wife’s main machine for a time, and lately my youngest daughter has been doing all her homework on it. Even in retirement it worked hard for it’s living.

I figure it must be 12 years old, and when it finally failed it was still running Ubuntu 11.04, which is a sophisticated and current operating system. Ok, the bizarre hybrid sound card wasn’t recognised (the 600 used a custom DSP to implement the modem and the sound system – a great idea, badly executed) and it wasn’t the fastest system on the block, but the overall experience was still pretty good.

At the end of the day it’s just a pile of electronics attached to a magnesium alloy chassis with some rather drab composite plastic covers, that no longer works. I should just recycle it. But there is an emotional attachment; I can’t bring myself to just take it to the recycling centre and dump it. But given that the motherboard has failed, the best I can offer it is the chance to donate some spare parts to new projects. So for now it’s going into my spare parts box; hopefully the screen, memory, disk and perhaps keyboard will show up in some future projects.

It may yet live again!

The MRI scans showed that the kidney was still a little distended, which generally indicates problems with the drainage from the kidney to the bladder, via the ureter. In my case, although the kidney is looking much better, my consultant suspects there is still a problem where my left ureter crosses my pelvic inlet, and that there is some constriction there causing the slow drainage to my bladder.

To prove this, my Urologist is going to run an intravenous urogram or IVU. The good news is it’s basically nothing I’ve not been through already, several times over. The bad news? Another cannula, and some of that “hot flush” iodine contrast agent. Still, it should take no more than an hour or so, and if it helps them resolve the problem, then fine. At a minimum it will be good to understand exactly what the problem is, and what they can do to fix it.

Because from what the consultants have told me so far, they are all happy with my progress, so hopefully this is just one more step closer to finally getting that clean bill of health.

The hernia seems to have stabilised, which is positive, but it’s still a real nuisance to live with, and isn’t going to get better any time soon. Ups and downs and guess.

The problem however, is the physical trauma to the stoma, which has continued to get slowly worse. So at the start of this week I booked an appointment with the Stoma Nurses, to see if they can offer some help. They tell me that all the problems I’m seeing are common, so hopefully they will have some solutions for them.

I’ll find out when I see them on Wednesday morning.

Of course, I get the odd cold, run a bit of a temperature, pull the odd muscle, get headaches, and have unexplained aches and pains just like anyone else of my age.

And I understand that – I’m not a hypochondriac. But my reaction to these things is not very logical. Frankly it’s anything but – which is difficult to explain to people. And then I saw this cartoon, which explains everything. Enjoy.

This post is all about the same attempt, but this time with the Gnome 3 Shell.

So, having freshly installed Ubuntu 11.10, we need to install Gnome Shell. It’s in the repositories, so it’s a simple matter of opening a terminal and issuing the command:
sudo apt-get install gnome-shell

The steps I then followed were:

1. Getting to a shell prompt with Alt + F2 has been disabled by default in Gnome Shell under Ubuntu 11.10. This is annoying, as it means you can’t (trivially) restart or debug the desktop environment without it. To fix it, open “System Settings” and under the Keyboard settings, go to Shortcuts, then System, and then click the “Disabled” next to “Show the run command prompt” and press Alt + F2 to re-enable the command prompt.
2. Next I added some Gnome Shell customisations from http://extensions.gnome.org, which make Gnome Shell look a lot more like Gnome 2. Heretical? Perhaps. So shoot me.
   1. Frippery Applications Menu – puts an old-school applications menu on the left side of the top menu
   2. Frippery Bottom Panel – adds a taskbar to the bottom of every workspace
   3. Frippery Move Clock – moves the clock back to where it used to be in Gnome 2.xx
   4. Frippery Panel Favorite – adds a copy of the launcher into the top panel
3. Next, I wanted to remove the accessibility icon from the top panel. Last time I looked, I didn’t need any of those settings, so I certainly don’t need the icon there all the time. To get rid of it, I downloaded an extension from the website of the author of all the previous extensions:
   http://www.fpmurphy.com/gnome-shell-extensions/noa11y-2.0.tar.gz

   This needs to be unpacked into ~/.local/share/gnome-shell/extensions/ by cd’ing to that directory and running something like:
   tar xvf ~/Downloads/noa11y-2.0.tar.gz.

   You then need to install Gnome Tweak to be able to enable the extension:
   sudo apt-get install gnome-tweak-tool
   and then run it with gnome-tweak-tool and choose to enable or disable whatever extensions you have loaded.

4. As with Unity, I wanted to disable the overlay scrollbars:
   sudo su
echo "export LIBOVERLAY_SCROLLBAR=0" > /etc/X11/Xsession.d/80overlayscrollbars


   Sadly the scrollbars still don’t have scroll buttons on them – which reinforces my thought that this is simply an issue with themes, and hence can probably be resolved once I’ve learned how themes work.

5. Next, move my preferred set of three window buttons back to the top right of each window titlebar by running the command:
   
gconftool-2 --set --type str /desktop/gnome/shell/windows/button_layout ":minimize,maximize,close"

6. Around now it’s probably worthwhile to logout and back in again, or even reboot.

7. Next I configured the general settings:

   1. Screen:
      Turn off at “30 minutes”
      Set screen lock “on” after “screen turns off”
   2. Power:
      Do nothing when lid closed (battery or AC)
      Don’t suspend when inactive (battery or AC)
      Shutdown if power critical on battery
   3. Time and Date:
      Panel clock to show 12hour format
   4. Removable Media:
      Tick “Never prompt or start programs on media insertion”

8. Next I added the date to the clock:
   gsettings set org.gnome.shell.clock show-date true


9. As with Unity, I configured the terminal by opening terminal preferences, and set the font to “Monospace 9″, the default terminal size to 100×40, and the scrollback to 10000 lines.

10. As with Unity, I changed the default fonts throughout:
    
gsettings set org.gnome.desktop.interface document-font-name 'Sans 10'
gsettings set org.gnome.desktop.interface font-name 'Ubuntu 9'
gsettings set org.gnome.desktop.interface monospace-font-name 'Ubuntu Mono 10'
gsettings set org.gnome.nautilus.desktop font 'Ubuntu 10'
gconftool --set /apps/metacity/general/titlebar_font 'Ubuntu Bold 9' --type STRING


11. I also removed the guest account:
    
sudo gedit /etc/lightdm/lightdm.conf

    Make it read:
    
[SeatDefaults]
greeter-session=unity-greeter
user-session=ubuntu
allow-guest=false


12. At this point I found I had a desktop that had almost all the features of my current Gnome 2 setup, plus access to the new metaphor of the Gnome Shell when I wanted it. The only problem is that when mousing to the newly added Applications menu, it’s far too easy to hit the “hot spot”, triggering the Overview Mode.

    There are extensions to move that hotspot elsewhere, but I’d prefer to change the way it works, so it takes a more conscious effort to engage it. Unfortunately there is no configuration for this, so for this exercise I took a quick hack at the base code, which is a real cludge. I’m hopeful that it may be possible to do something cleaner with Monkey patching, but for now my change proves the concept, and makes it necessary to click on the hotspot to engage it, or use the super key (as now). To do this, edit:
    /usr/share/gnome-shell/js/ui/layout.js, and change the _onCornerEntered method so it reads:

    
_onCornerEntered : function() {
// if (!this._entered) {
// Patched this to prevent the hot corner from engaging on cursor entering zone.
if (this._entered) {
this._entered = true;
if (!Main.overview.animationInProgress) {
this._activationTime = Date.now() / 1000;

    this.rippleAnimation();
Main.overview.toggle();
}
}
return false;
},


    Now just entering the hotspot will not trigger the Overview Mode – but you can still click on the hotspot (which is the top left pixel), or just use the Super key.

13. Since I was messing around in the source code I also decided to get rid of the “currently running application name” in the top panel, which again cannot be configured away. Quite why I’d need to be reminded of the name of the application I’m using is beyond me, and it takes up precious menubar space. This time, edit:

    /usr/share/gnome-shell/js/ui/panel.js, and find the AppMenuButton function prototype. Then scroll down to the “_sync” method, and make the first few lines read:
    
_sync: function() {
let tracker = Shell.WindowTracker.get_default();
let lastStartedApp = null;
let workspace = global.screen.get_active_workspace();
// Add the following line to never show the button (application name)
return;
for (let i = 0; i < this._startingApps.length; i++)
if (this._startingApps[i].is_on_workspace(workspace))
lastStartedApp = this._startingApps[i];


    This works perfectly, but like the previous code change, the problem is that whenever Gnome Shell gets updated, I would need to re-hack these changes manually. Which is not good. But as I mentioned before, I’m hopeful that Monkey Patching will come to the rescue and allow me to create a proper extension for this.

And the conclusion? Well, since it’s all written in Javascript and CSS, Gnome Shell is much easier to customise, and its extension system allows (in theory) for a robust and user-friendly mechanism to change anything that one wishes. I now have a DE that has all the features I like from an “old” Gnome 2 desktop, as well as access to all the new features of Gnome Shell. See below:

There are still rough edges, some of which are probably bugs too, but overall I can get closer to what I want (which may not be what you, or the Gnome Shell developers want) with Gnome Shell than Unity.

So when I upgrade my work “production” laptop over Christmas, it will be to a Gnome Shell based desktop.

Which gives me a pretty strong push back towards finding a way to make Unity somewhat more palatable and productive. So I’ve set about trying to turn Unity into something that I can live with for work. I’d not say I’ve completely achieved that yet, but a couple of (long) evenings have got me a fair way forward, and revealed a few problems that I probably need to raise as bugs against Unity – though given the non-standard way that I’ve exposed them, it’s debatable whether they’ll ever be addressed or not. Anyway, here are the results so far:

My normal desktop

Customised Oneiric, with the launcher open

Customised Oneiric, with application selector open

And this is what I did to a freshly installed Ubuntu 11.10 system to get there:

1. Add back a menu of applications that can act as a launcher, and a taskbar where I can see what I have running. I came across this post describing how to resolve these issues, and merely followed the directions.

   First the menu launcher:
   
sudo add-apt-repository ppa:diesch/testing
sudo apt-get update
sudo apt-get install classicmenu-indicator


   Once installed, run it by pressing Alt-F2 and typing classicmenu-indicator.

   Now install the taskbar:
   
sudo apt-get install tint2


   Once installed, set it to auto-run on system start, by adding an entry to the Startup Applications. The executable is at /usr/bin/tint2. Then configure the resulting bottom panel (in ~/.config/tint2/tint2rc) so it only has a taskbar, removing the clock and battery indicators, by adding:
   panel_items = T
   and adjust its size to avoid interference with the unity launcher (when it’s on screen) by making sure:
   panel_size = 90% 30
   and finally (a personal choice) remove the ability to close applications from the taskbar by setting:
   mouse_right = none

2. Next, get rid of the ugly Unity launcher by making it autohide. This is done by altering some parameters in the Unity plugin in compiz. You need to install Compiz Config Settings Manager (CCSM) first, by:

   sudo apt-get install compizconfig-settings-manager

   Then run it with ccsm, and find and select the Unity plugin. Then on the Behaviour tab:
   
   Set “Hide Launcher” to “Autohide”
   
   Set “Edge Reveal Timeout” to 100
   
   On the Experimental tab:
   
   Set “Backlight mode” to “Edge Illumination Toggles”
   
   Set “Launcher Icon Size” to 32
   
   Set “Launcher Opacity” to “0.8000″

   I still think it looks like it was designed by a child with a set of blunt crayons, but this makes it a bit more professional-looking, and since it’s now going to be hidden most of the time (and rarely used) I can live with it. I do wish there was an option to completely disable it though.

3. Next I fixed the window buttons, by re-enabling the standard minimise, maximise, close triple, and moving them to the right side of the window title bar. Do this by entering:

   gconftool-2 --set /apps/metacity/general/button_layout --type string ":minimize,maximize,close"

4. Then I disabled the ridiculous Overlay Scrollbars, and the Global Menu; together this moves the window buttons and menus back onto the windows where they belong, and gives us working scrollbars on all applications again, including those that are built on Eclipse:

   sudo su
echo "export LIBOVERLAY_SCROLLBAR=0" > /etc/X11/Xsession.d/80overlayscrollbars
echo "export UBUNTU_MENUPROXY=0" > /etc/X11/Xsession.d/81ubuntumenuproxy

   Sadly the scrollbars lack scroll buttons; I’ve not worked out how to resolve this yet, which can make fine positioning difficult. But it’s orders of magnitude easier than fighting with the overlay scrollbars.

5. Firefox has an extension to separately move its menus to Unitys top panel, and this needs to be disabled too. Access it from Firefox’s Tools->AddOns menu. It seems to require that Firefox be restarted, and a logout/login sequence to be followed before it fully takes effect.
6. Next I took back control of the workspaces, by adding an indicator applet into the notification area of the top panel, that also functions as a workspace switcher. The indicator is in a PPA, but unfortunately only for Natty rather than Oneiric. The Natty version works just fine under Oneiric, and installing it is straightforward, if a little fiddly, by following these instructions.

7. At this point I rebooted to make sure everything was working, and noticed that the classic menu indicator was not the leftmost of my indicators any more. However, it is possible to specify the exact ordering of indicators, so I reordered mine by:

   
mkdir -p ~/.local/share/indicators/application
cp /usr/share/indicator-application/ordering-override.keyfile ~/.local/share/indicators/application/


   Editing the new local ordering-override.keyfile allows the exact order of the indicators to be specified. Lowest numbers are to the right of the panel. To find the id of unknown indicators, use:
   
dbus-send --type=method_call --print-reply \
--dest=com.canonical.indicator.application \
/com/canonical/indicator/application/service \
com.canonical.indicator.application.service.GetApplications | grep "object path"


   This results in lines like:
   object path "/org/ayatana/NotificationItem/gnome_power_manager/Menu"
   In this case, the id is gnome-power-manager, but note that the command output contains underscores which need to be changed to dashes to be valid in the ordering-override.keyfile.

8. Next I installed dconf-editor, which allows a few additional tweaks to be make to Unity:
   
sudo apt-get install dconf-tools


9. I then did some configuration of general settings around the operating system. First, I configured the terminal look and feel by opening terminal preferences:
   
Set font to "Monospace 9"
Set default size to 100x40
Set scrollback to 10000


   Next I changed all the fonts throughout the system, as the defaults seem far too large:
   
gsettings set org.gnome.desktop.interface document-font-name 'Sans 10'
gsettings set org.gnome.desktop.interface font-name 'Ubuntu 9'
gsettings set org.gnome.desktop.interface monospace-font-name 'Ubuntu Mono 10'
gsettings set org.gnome.nautilus.desktop font 'Ubuntu 10'
gconftool --set /apps/metacity/general/titlebar_font 'Ubuntu Bold 9' --type STRING


   Then, in the “Screen” settings, I configured the screen to turn off at “30 minutes”, and set the screen lock “on” after the “screen turns off”. In the “Power” settings I set the system to “Do nothing” when the lid is closed (on battery or AC), and not to suspend when inactive (on battery or AC), but to shutdown when power is critically short on battery. In the Time and Date settings I set the Panel clock to show the Date and Month, and the clock in 12 hour format. Finally, in “Removable Media” I set the system to never prompt or start programs on media insertion.

10. To add a quick list of locations to the Launcher “files” icon, I ran the following as a single command:
    
echo "[Desktop Entry]

    Name=Home Folder
    Comment=Open your personal folder
    TryExec=nautilus
    Exec=nautilus --no-desktop
    Icon=user-home
    Terminal=false
    StartupNotify=true
    Type=Application
    Categories=GNOME;GTK;Core;
    OnlyShowIn=GNOME;Unity;
    X-GNOME-Bugzilla-Bugzilla=GNOME
    X-GNOME-Bugzilla-Product=nautilus
    X-GNOME-Bugzilla-Component=general
    X-Ubuntu-Gettext-Domain=nautilus
    X-Ayatana-Desktop-Shortcuts=Videos;Documents;Music;Pictures;Downloads

    [Videos Shortcut Group]
    Name=Videos
    Exec=nautilus Videos
    TargetEnvironment=Unity

    [Documents Shortcut Group]
    Name=Documents
    Exec=nautilus Documents
    TargetEnvironment=Unity

    [Music Shortcut Group]
    Name=Music
    Exec=nautilus Music
    TargetEnvironment=Unity

    [Pictures Shortcut Group]
    Name=Pictures
    Exec=nautilus Pictures
    TargetEnvironment=Unity

    [Downloads Shortcut Group]
Name=Downloads
Exec=nautilus Downloads
TargetEnvironment=Unity" | sudo tee /usr/share/applications/nautilus-home.desktop


11. Next I disabled the guest account in LightDM. This prevents someone from logging into my machine (albeit with very limited privileges) when I’m away from the machine. I suspect our security people would not be comfortable with this feature left enabled. To do this, edit /etc/lightdm/lightdm.conf, and make it read:
    
[SeatDefaults]
greeter-session=unity-greeter
user-session=ubuntu
allow-guest=false


12. Next I wanted to change the Alt-PrtSc capability, so I can capture a specific area if the screen rather than the active window. I want to retain the default PrtSc functionality. To do this, I started ccsm, and in the Gnome Compatibility plugin I changed the command “gnome-screenshot -w” (active window) to “gnome-screenshot –area”.

    While I was in ccsm I also disabled the “Snapping Windows” plugin, as it was driving me nuts. I also set a key combination (Ctl-Alt-g) on the “Toggle Handles” option of the Unity MT Grab Handles plugin, to allow easier screen grabbing & manipulation, as the default theme has quite small borders to its windows.

13. By default, Oneiric doesn’t come with any screensavers. It simply fades to black. Which is efficient, but rather boring. So I removed the default screensaver (which does nothing) and reenabled all the pretty screensavers:
    
sudo apt-get remove --purge gnome-screensaver
sudo apt-get install xscreensaver xscreensaver-gl-extra xscreensaver-data-extra


    It’s then necessary to add “xscreensaver -nosplash” to the startup applications. This is the server portion of the screensaver which does the actual displaying of the animations, the locking of the screen, and any power management. It’s configured with “xscreensaver-demo”, which allows graphical selection of screensaver animations etc. Finally, to keep the ctl-alt-L key combination to manually start the screensaver, it’s necessary to:
    
sudo ln -s /usr/bin/xscreensaver-command /usr/bin/gnome-screensaver-command


14. Getting Conky installed (to create the animated desktop) was simple, once I’d realised that the key to making it work under Unity is to change the .conkyrc configuration stanza to own_window_type normal. However, Unity does something odd with painting itself into a different window than the root, so Conky cannot do transparent without help from something like feh, but that can only work with static images, not my preferred gradient fill. I resolved the issue by adopting an image for my desktop background.

15. Finally, I mentioned a few issues that I’d not resolved yet:
    
    It seems impossible to stop the Unity top panel showing the name of the active applicaton.
    
    It seems impossible to move the classicmenu_indicator to the left of the Unity top panel.
    
    Having disabled the overlay scrollbars, the remaining scrollbars lack scroll buttons
    
    It seems impossible to remove the workplace switcher icon from the Unity Dash (hard-coded) Raised as Bug 898230.
    
    It seems impossible to remove the Dash Home icon from the Unity Dash (Hard-coded) Raised as Bug 898230.
    
    When maximising a window, Unity still steals the window buttons, and places them in its top panel Raised as Bug 898250.
    
    When stealing the window buttons, it doesn’t adhere to the setting in gconf for how to display them, but uses a hardcoded default Raised as Bug 898250.
    
    Seems to be impossible to completely disable the Unity Launcher Raised as Bug 898260.

    Help with any of the above would be much appreciated!